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Sample GSM90629 Query DataSets for GSM90629
Status Public on Jan 05, 2006
Title liver cell line
Sample type RNA
 
Channel 1
Source name stratagene mouse reference
Organism Mus musculus
Characteristics stratagene mouse reference
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name liver cell line
Organism Mus musculus
Characteristics liver cell line
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tissue, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20340.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Jan 04, 2006
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL3304
Series (2)
GSE3974 Contribution of unique genes by individual cell lines to Universal Mouse Reference RNA
GSE4389 Universal Reference RNA as a standard for microarray experiments

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high LOG_RAT2N_MEDIANs imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
VALUE Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2
LOG_RAT2N_MEDIAN Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN VALUE LOG_RAT2N_MEDIAN
1 39074 34982 471 670 38603 34312 47078 40140 523 727 46607 39470 3 0 21236 18731 245 365 93 93 91 91 72915 86077 1.125 .889 .847 1 .893 1.823 156 845 .885 .99 150 2840 3980 38 53 68 83 0 32693 626 32067 .831 37514 36888 1.204 .791 -.268 -.337
2 1587 1458 360 513 1227 945 1643 1497 408 553 1283 984 0 0 703 680 203 280 85 82 83 68 2172 2267 1.298 .77 .767 .729 .769 2.085 156 651 .877 .81 150 3020 3980 38 53 86 101 0 1363 479 883 .72 1399 920 1.389 .717 -.474 -.48
3 1326 1327 350 489 976 838 1214 1275 399 552 864 786 0 0 1130 872 209 320 81 73 74 60 1814 1650 1.165 .859 .91 .95 .976 2.66 156 648 .807 .84 150 3210 3990 39 54 105 120 -100 1240 457 783 .802 1192 735 1.246 .85 -.318 -.234
4 4903 3558 323 483 4580 3075 5139 3672 355 540 4816 3189 0 0 2393 1661 158 306 92 91 91 88 7655 8005 1.489 .671 .662 .714 .698 1.82 156 651 .675 .9 150 3410 3980 38 53 125 140 0 3325 451 2874 .627 3432 2980 1.594 .619 -.672 -.692
5 1378 1581 309 477 1069 1104 1512 1719 344 521 1203 1242 0 0 820 898 156 273 74 72 71 66 2173 2445 .968 1.033 1.032 1.149 1.105 2.099 208 728 1.118 .84 160 3590 3980 38 54 143 159 0 1478 446 1032 .965 1607 1161 1.036 .965 -.051 -.052
6 1034 823 321 484 713 339 1126 742 356 522 805 258 0 0 683 592 166 255 70 50 65 27 1052 1063 2.103 .475 .32 .678 .606 3.628 208 682 .702 .63 160 3780 3980 38 54 162 178 -100 769 452 317 .444 693 241 2.25 .3 -1.17 -1.739
7 6860 8652 325 482 6535 8170 7495 9722 359 559 7170 9240 0 0 5287 6572 173 344 76 74 72 71 14705 16410 .8 1.25 1.289 1.39 1.282 1.927 208 701 1.257 .97 160 3970 3980 38 54 181 197 0 8086 450 7636 1.168 9086 8636 .856 1.204 .225 .268
8 3467 5263 318 468 3149 4795 4058 5607 344 547 3740 5139 0 0 2571 3854 147 446 74 73 71 69 7944 8879 .657 1.523 1.374 1.656 1.543 1.882 208 665 1.532 .97 160 4160 3990 39 55 200 216 0 4919 437 4481 1.423 5240 4803 .703 1.284 .509 .361
9 1573 1765 314 464 1259 1301 1654 1860 356 538 1340 1396 0 0 1052 1104 414 452 66 68 61 60 2560 2736 .968 1.033 1.042 1.171 1.092 2.113 208 661 1.066 .9 160 4350 3980 38 54 219 235 0 1650 434 1216 .966 1738 1305 1.035 .974 -.05 -.039
10 667 637 304 448 363 189 668 570 347 515 364 122 0 0 349 326 424 316 42 28 8 8 552 486 1.921 .521 .335 .666 .729 3.719 208 633 1.02 .41 160 4540 3990 39 55 238 254 0 595 419 177 .487 533 114 2.055 .313 -1.039 -1.675
11 951 852 295 429 656 423 1061 777 325 483 766 348 0 0 531 458 163 335 70 50 63 27 1079 1114 1.551 .645 .454 .69 .674 2.89 208 689 1.081 .62 160 4730 3990 39 55 257 273 0 796 401 395 .603 726 325 1.659 .425 -.731 -1.236
12 631 646 289 437 342 209 501 581 319 480 212 144 0 0 366 377 133 300 58 33 46 14 551 356 1.636 .611 .679 .895 .852 3.622 156 526 1.241 .54 140 4920 3990 40 54 277 291 0 604 408 195 .571 543 135 1.751 .635 -.808 -.656
13 2265 2068 298 450 1967 1618 2592 2187 330 484 2294 1737 0 0 1561 1371 167 280 74 73 70 67 3585 4031 1.216 .823 .757 .971 .887 2.389 208 694 .848 .91 160 5110 3990 39 55 295 311 0 1933 421 1512 .769 2044 1623 1.301 .708 -.379 -.499
14 1124 695 293 440 831 255 1156 664 325 487 863 224 0 0 440 295 156 267 90 41 87 15 1086 1087 3.259 .307 .26 .335 .349 2.782 156 618 .4 .47 150 5300 3990 39 54 314 329 0 650 411 238 .287 621 209 3.487 .243 -1.802 -2.043
15 1157 1253 292 453 865 800 1251 1257 320 496 959 804 0 0 692 738 157 255 73 73 71 61 1665 1763 1.081 .925 .838 .979 .988 2.211 208 753 1.099 .75 160 5500 3990 39 55 334 350 0 1171 423 748 .864 1175 751 1.157 .784 -.21 -.352
16 2421 2475 295 443 2126 2032 2517 2449 323 478 2222 2006 0 0 1059 1196 155 233 93 94 92 87 4158 4228 1.046 .956 .903 .908 .93 1.669 156 621 1.002 .91 150 5680 3990 39 54 352 367 0 2313 414 1899 .893 2289 1875 1.119 .844 -.163 -.245
17 774 709 310 459 464 250 786 638 333 503 476 179 0 0 411 369 140 271 73 42 68 20 714 655 1.856 .539 .376 .656 .701 3.509 208 856 .935 .43 160 5870 3980 38 54 371 387 0 663 429 234 .504 596 167 1.986 .351 -.99 -1.509
18 1029 1271 337 597 692 674 1031 1346 353 608 694 749 0 0 475 669 131 253 90 72 72 58 1366 1443 1.027 .974 1.079 1.12 1.044 2.027 80 429 1.38 .71 110 6050 3990 41 52 391 402 0 1188 558 630 .91 1258 700 1.099 1.009 -.136 .012
19 1293 1451 311 468 982 983 1439 1456 339 513 1128 988 0 0 753 822 162 262 76 74 71 65 1965 2116 .999 1.001 .876 1.063 1.04 2.541 208 834 1.077 .83 160 6250 4000 40 56 409 425 0 1356 437 919 .936 1361 923 1.069 .819 -.096 -.289
20 952 1067 296 419 656 648 888 917 327 465 592 498 0 0 498 713 170 265 82 66 68 49 1304 1090 1.012 .988 .841 .909 .903 2.845 156 614 1.511 .63 150 6440 4000 40 55 428 443 0 997 392 606 .923 857 465 1.083 .786 -.115 -.347

Total number of rows: 7680

Table truncated, full table size 1772 Kbytes.




Supplementary data files not provided
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